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Rename SWRL variables to use valid URN format. #776

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Dec 15, 2023
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Rename SWRL variables to use valid URN format. #776

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32 changes: 16 additions & 16 deletions src/ontology/ro-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -7113,25 +7113,25 @@ SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0013007 obo:BFO_0000050) obo:RO_0
SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0015001 obo:RO_0015003) obo:RO_0015001)
SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(obo:BFO_0000066) obo:RO_0002234) obo:RO_0003000)
SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(obo:RO_0002176) obo:RO_0002176) obo:RO_0002170)
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002180 Variable(<urn:swrl#w>) Variable(<urn:swrl#p>)) ClassAtom(obo:BFO_0000015 Variable(<urn:swrl#w>)) ClassAtom(obo:BFO_0000015 Variable(<urn:swrl#p>)))Head(ObjectPropertyAtom(obo:RO_0002018 Variable(<urn:swrl#w>) Variable(<urn:swrl#p>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002180 Variable(<urn:swrl:var#w>) Variable(<urn:swrl:var#p>)) ClassAtom(obo:BFO_0000015 Variable(<urn:swrl:var#w>)) ClassAtom(obo:BFO_0000015 Variable(<urn:swrl:var#p>)))Head(ObjectPropertyAtom(obo:RO_0002018 Variable(<urn:swrl:var#w>) Variable(<urn:swrl:var#p>))))
DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom(obo:RO_0002327 Variable(<http://purl.obolibrary.org/obo/ro.owl#z>) Variable(<http://purl.obolibrary.org/obo/ro.owl#y>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<http://purl.obolibrary.org/obo/ro.owl#x>) Variable(<http://purl.obolibrary.org/obo/ro.owl#y>)) ClassAtom(obo:GO_0003674 Variable(<http://purl.obolibrary.org/obo/ro.owl#x>)) ClassAtom(obo:GO_0003674 Variable(<http://purl.obolibrary.org/obo/ro.owl#y>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<http://purl.obolibrary.org/obo/ro.owl#x>) Variable(<http://purl.obolibrary.org/obo/ro.owl#z>))))
DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom(obo:GO_0003674 Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:BFO_0000051 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom(obo:GO_0008150 Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:BFO_0000050 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ObjectPropertyAtom(obo:RO_0002331 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Annotation(rdfs:seeAlso <https://github.com/oborel/obo-relations/issues/259>) Body(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#a1>) Variable(<urn:swrl#a2>)) ClassAtom(obo:GO_0016301 Variable(<urn:swrl#a1>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#a1>) Variable(<urn:swrl#g1>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#a2>) Variable(<urn:swrl#g2>)))Head(ObjectPropertyAtom(obo:RO_0002447 Variable(<urn:swrl#g1>) Variable(<urn:swrl#g2>))))
DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl#B>) Variable(<urn:swrl#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#A>) Variable(<urn:swrl#B>)) ObjectPropertyAtom(obo:RO_0002013 Variable(<urn:swrl#D>) Variable(<urn:swrl#C>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#A>) Variable(<urn:swrl#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl#B>) Variable(<urn:swrl#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#A>) Variable(<urn:swrl#B>)) ObjectPropertyAtom(obo:RO_0002014 Variable(<urn:swrl#D>) Variable(<urn:swrl#C>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#A>) Variable(<urn:swrl#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl#B>) Variable(<urn:swrl#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#A>) Variable(<urn:swrl#B>)) ObjectPropertyAtom(obo:RO_0002015 Variable(<urn:swrl#D>) Variable(<urn:swrl#C>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#A>) Variable(<urn:swrl#D>))))
DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#eff>) Variable(<urn:swrl#in>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#mf>) Variable(<urn:swrl#in>))))
DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#mf>) Variable(<urn:swrl#in>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#eff>) Variable(<urn:swrl#in>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002404 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl#x>))))
DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl#x>))))
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom(obo:GO_0003674 Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:BFO_0000051 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom(obo:GO_0008150 Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:BFO_0000050 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0002331 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Annotation(rdfs:seeAlso <https://github.com/oborel/obo-relations/issues/259>) Body(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl:var#a1>) Variable(<urn:swrl:var#a2>)) ClassAtom(obo:GO_0016301 Variable(<urn:swrl:var#a1>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl:var#a1>) Variable(<urn:swrl:var#g1>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl:var#a2>) Variable(<urn:swrl:var#g2>)))Head(ObjectPropertyAtom(obo:RO_0002447 Variable(<urn:swrl:var#g1>) Variable(<urn:swrl:var#g2>))))
DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl:var#B>) Variable(<urn:swrl:var#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#B>)) ObjectPropertyAtom(obo:RO_0002013 Variable(<urn:swrl:var#D>) Variable(<urn:swrl:var#C>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl:var#B>) Variable(<urn:swrl:var#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#B>)) ObjectPropertyAtom(obo:RO_0002014 Variable(<urn:swrl:var#D>) Variable(<urn:swrl:var#C>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl:var#B>) Variable(<urn:swrl:var#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#B>)) ObjectPropertyAtom(obo:RO_0002015 Variable(<urn:swrl:var#D>) Variable(<urn:swrl:var#C>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl:var#A>) Variable(<urn:swrl:var#D>))))
DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#in>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#in>))))
DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#in>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#in>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#mf2>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)) ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#mf2>))))
DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl:var#mf>) Variable(<urn:swrl:var#eff>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl:var#eff>) Variable(<urn:swrl:var#mf2>))))
DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002404 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl:var#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl:var#x>))))
DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl:var#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl:var#x>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002211 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012012 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0019002 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0019001 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002264 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0002263 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#q>) Variable(<urn:swrl:var#u>)))Head(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#u>))))
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